"Hyper-Speed" appears to just be a "deluxe" branding. Servers advertised as such will have better hardware than you might be used to seeing from Supermicro.
And one other thing, it appears that they've unlocked overclocking in the BIOS as seen in this article:
But all the overclocking options there are nothing fancy. They're the same type of overclocking options you'd find on any consumer-grade motherboard these days.
Does this affect the overall system stability?
Yes, overclocking can adversely affect overall system stability and hardware life span. Plus warranty and support options... but you probably don't care about those things if you're overclocking your servers. Overclocking is more of an enthusiast activity, not as much an IT pro one.
Today we are looking at the specific Supermicro Hyper-Speed BIOS
settings that allow the company to speed up the dual Intel Xeon E5
CPUs. In the consumer world, this type of activity is relegated to
mostly enthusiasts. The Supermicro Hyper-Speed line is significantly
different because the company pre-qualifies configurations and parts